The invention discloses a treatment method of microbial fermentation drug waste mushroom dregs. Waste mushroom dregs or turbid liquid of the waste mushroom dregs are collected through solid-liquid separation equipment, then closed heating treatment is conducted in high-temperature-resistant and high-pressure-resistant equipment to achieve reduction of solid matter, a product obtained after heatingtreatment is treated through the solid-liquid separation equipment, the obtained solid matter is packaged after being treated through drying equipment, and compliance treatment is conducted after hazardous waste identification; and biochemical degradation treatment is carried out on the obtained clear liquid. According to the method, the solid matter weight is remarkably reduced, then the aftertreatment cost is reduced, equipment and the method meet the GMP requirement, the process controllability is high, continuous treatment can be achieved, and the method is an efficient and safe mushroomdreg treatment way in the pharmaceutical industry.